Your comments

This is sort of inconvenient. The default setup for Ubuntu Server is to have the root user disabled, and I've never had any reason to change that on any of my servers.

The first thing I did after installing Ajenti was go to change the default account password. I saw the sync with OS users option and set that. That's how I ended up here five minutes after install. It may not be a bug but it's definitely not the best user experience. I feel maybe a warning to Ubuntu users when switching to this options would be nice.